Overview
Availability
- Honorary Professor Amanda Spurdle is:
- Available for supervision
Fields of research
Works
Search Professor Amanda Spurdle’s works on UQ eSpace
2024
Journal Article
Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 variant curation expert panel
Parsons, Michael T., de la Hoya, Miguel, Richardson, Marcy E., Tudini, Emma, Anderson, Michael, Berkofsky-Fessler, Windy, Caputo, Sandrine M., Chan, Raymond C., Cline, Melissa S., Feng, Bing-Jian, Fortuno, Cristina, Gomez-Garcia, Encarna, Hadler, Johanna, Hiraki, Susan, Holdren, Megan, Houdayer, Claude, Hruska, Kathleen, James, Paul, Karam, Rachid, Leong, Huei San, Martins, Alexandra, Mensenkamp, Arjen R., Monteiro, Alvaro N., Nathan, Vaishnavi, O'Connor, Robert, Pedersen, Inge Sokilde, Pesaran, Tina, Radice, Paolo, Schmidt, Gunnar ... Spurdle, Amanda B. (2024). Evidence-based recommendations for gene-specific ACMG/AMP variant classification from the ClinGen ENIGMA BRCA1 and BRCA2 variant curation expert panel. The American Journal of Human Genetics, 111 (9), 2044-2058. doi: 10.1016/j.ajhg.2024.07.013
2024
Journal Article
Co-observation of germline pathogenic variants in breast cancer predisposition genes: Results from analysis of the BRIDGES sequencing dataset
Davidson, Aimee L., Michailidou, Kyriaki, Parsons, Michael T., Fortuno, Cristina, Bolla, Manjeet K., Wang, Qin, Dennis, Joe, Naven, Marc, Abubakar, Mustapha, Ahearn, Thomas U., Alonso, M. Rosario, Andrulis, Irene L., Antoniou, Antonis C., Auvinen, Päivi, Behrens, Sabine, Bermisheva, Marina A., Bogdanova, Natalia V., Bojesen, Stig E., Brüning, Thomas, Byers, Helen J., Camp, Nicola J., Campbell, Archie, Castelao, Jose E., Cessna, Melissa H., Chang-Claude, Jenny, Chanock, Stephen J., Chenevix-Trench, Georgia, Sahlberg, Kristine K., Børresen-Dale, Anne-Lise ... kConFab Investigators (2024). Co-observation of germline pathogenic variants in breast cancer predisposition genes: Results from analysis of the BRIDGES sequencing dataset. The American Journal of Human Genetics, 111 (9), 2059-2069. doi: 10.1016/j.ajhg.2024.07.004
2024
Journal Article
Regional-specific calibration enables application of computational evidence for clinical classification of 5′ cis-regulatory variants in Mendelian disease
Villani, Rehan M., McKenzie, Maddison E., Davidson, Aimee L. and Spurdle, Amanda B. (2024). Regional-specific calibration enables application of computational evidence for clinical classification of 5′ cis-regulatory variants in Mendelian disease. American Journal of Human Genetics, 111 (7), 1301-1315. doi: 10.1016/j.ajhg.2024.05.002
2024
Journal Article
Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines
Fortuno, Cristina, Michailidou, Kyriaki, Parsons, Michael, Dolinsky, Jill S., Pesaran, Tina, Yussuf, Amal, Mester, Jessica L., Hruska, Kathleen S., Hiraki, Susan, O'Connor, Robert, Chan, Raymond C., Kim, Serra, Tavtigian, Sean, Goldgar, David, James, Paul A. and Spurdle, Amanda B. (2024). Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines. Human Molecular Genetics, 33 (8), 724-732. doi: 10.1093/hmg/ddae009
2023
Journal Article
The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants—a multi-site prospective cohort study
Davidson, Aimee L., Dressel, Uwe, Norris, Sarah, Canson, Daffodil M., Glubb, Dylan M., Fortuno, Cristina, Hollway, Georgina E., Parsons, Michael T., Vidgen, Miranda E., Holmes, Oliver, Koufariotis, Lambros T., Lakis, Vanessa, Leonard, Conrad, Wood, Scott, Xu, Qinying, McCart Reed, Amy E., Pickett, Hilda A., Al-Shinnag, Mohammad K., Austin, Rachel L., Burke, Jo, Cops, Elisa J., Nichols, Cassandra B., Goodwin, Annabel, Harris, Marion T., Higgins, Megan J., Ip, Emilia L., Kiraly-Borri, Catherine, Lau, Chiyan, Mansour, Julia L. ... Ward, Robyn L. (2023). The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants—a multi-site prospective cohort study. Genome Medicine, 15 (1) 74, 1-16. doi: 10.1186/s13073-023-01223-1
2023
Journal Article
Design and quality control of large-scale two-sample Mendelian randomization studies
Haycock, Philip C, Borges, Maria Carolina, Burrows, Kimberley, Lemaitre, Rozenn N, Harrison, Sean, Burgess, Stephen, Chang, Xuling, Westra, Jason, Khankari, Nikhil K, Tsilidis, Kostas K, Gaunt, Tom, Hemani, Gibran, Zheng, Jie, Truong, Therese, O'Mara, Tracy A, Spurdle, Amanda B, Law, Matthew H, Slager, Susan L, Birmann, Brenda M, Saberi Hosnijeh, Fatemeh, Mariosa, Daniela, Amos, Christopher I, Hung, Rayjean J, Zheng, Wei, Gunter, Marc J, Davey Smith, George, Relton, Caroline and Martin, Richard M (2023). Design and quality control of large-scale two-sample Mendelian randomization studies. International Journal of Epidemiology, 52 (5), 1498-1521. doi: 10.1093/ije/dyad018
2023
Journal Article
Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup
Walker, Logan C., Hoya, Miguel de la, Wiggins, George A R, Lindy, Amanda, Vincent, Lisa M., Parsons, Michael T., Canson, Daffodil M., Bis-Brewer, Dana, Cass, Ashley, Tchourbanov, Alexander, Zimmermann, Heather, Byrne, Alicia B., Pesaran, Tina, Karam, Rachid, Harrison, Steven M., Spurdle, Amanda B. and ClinGen Sequence Variant Interpretation Working Group (2023). Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. American Journal of Human Genetics, 110 (7), 1046-1067. doi: 10.1016/j.ajhg.2023.06.002
2023
Journal Article
The association between genetically elevated polyunsaturated fatty acids and risk of cancer
Tintle, Nathan, Rice, Terri, Cheng, Iona, Jenkins, Mark, Gallinger, Steve, Cornish, Alex J., Sud, Amit, Vijayakrishnan, Jayaram, Wrensch, Margaret, Johansson, Mattias, Norman, Aaron D., Klein, Alison, Clay-Gilmour, Alyssa, Franke, Andre, Ardisson Korat, Andres V., Wheeler, Bill, Nilsson, Björn, Smith, Caren, Heng, Chew-Kiat, Song, Ci, Riadi, David, Claus, Elizabeth B., Ellinghaus, Eva, Ostroumova, Evgenia, Hosnijeh,, de Vathaire, Florent, Cugliari, Giovanni, Matullo, Giuseppe, Oi-Lin Ng, Irene ... Martin, Richard M. (2023). The association between genetically elevated polyunsaturated fatty acids and risk of cancer. eBioMedicine, 91 104510. doi: 10.1016/j.ebiom.2023.104510
2023
Journal Article
Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genes
Canson, Daffodil M., O’Mara, Tracy A., Spurdle, Amanda B. and Glubb, Dylan M. (2023). Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genes. Human Genetics and Genomics Advances, 4 (2) 100185, 1-7. doi: 10.1016/j.xhgg.2023.100185
2023
Journal Article
SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion
Canson, Daffodil M., Davidson, Aimee L., de la Hoya, Miguel, Parsons, Michael T., Glubb, Dylan M., Kondrashova, Olga and Spurdle, Amanda B. (2023). SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion. Bioinformatics, 39 (4) btad179, 1-3. doi: 10.1093/bioinformatics/btad179
2022
Journal Article
Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars
Canson, Daffodil, Glubb, Dylan and Spurdle, Amanda B. (2022). Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Human Mutation, 43 (12), 2328-2328. doi: 10.1002/humu.24500
2022
Journal Article
Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation
Tudini, Emma, Andrews, James, Lawrence, David M., King-Smith, Sarah L., Baker, Naomi, Baxter, Leanne, Beilby, John, Bennetts, Bruce, Beshay, Victoria, Black, Michael, Boughtwood, Tiffany F., Brion, Kristian, Cheong, Pak Leng, Christie, Michael, Christodoulou, John, Chong, Belinda, Cox, Kathy, Davis, Mark R., Dejong, Lucas, Dinger, Marcel E., Doig, Kenneth D., Douglas, Evelyn, Dubowsky, Andrew, Ellul, Melissa, Fellowes, Andrew, Fisk, Katrina, Fortuno, Cristina, Friend, Kathryn, Gallagher, Renee L. ... and on behalf of the Shariant Consortium (2022). Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. American Journal of Human Genetics, 109 (11), 1960-1973. doi: 10.1016/j.ajhg.2022.10.006
2022
Journal Article
The splicing effect of variants at branchpoint elements in cancer genes
Canson, Daffodil M., Dumenil, Troy, Parsons, Michael T., O'Mara, Tracy A., Davidson, Aimee L., Okano, Satomi, Signal, Bethany, Mercer, Tim R., Glubb, Dylan M. and Spurdle, Amanda B. (2022). The splicing effect of variants at branchpoint elements in cancer genes. Genetics in Medicine, 24 (2), 398-409. doi: 10.1016/j.gim.2021.09.020
2021
Journal Article
Germline and Tumor Sequencing as a Diagnostic Tool To Resolve Suspected Lynch Syndrome
Pope, Bernard J., Clendenning, Mark, Rosty, Christophe, Mahmood, Khalid, Georgeson, Peter, Joo, Jihoon E., Walker, Romy, Hutchinson, Ryan A., Jayasekara, Harindra, Joseland, Sharelle, Como, Julia, Preston, Susan, Spurdle, Amanda B., Macrae, Finlay A., Win, Aung K., Hopper, John L., Jenkins, Mark A., Winship, Ingrid M. and Buchanan, Daniel D. (2021). Germline and Tumor Sequencing as a Diagnostic Tool To Resolve Suspected Lynch Syndrome. Journal of Molecular Diagnostics, 23 (3), 358-371. doi: 10.1016/j.jmoldx.2020.12.003
2021
Journal Article
The Impact of Variants at Branchpoint Splicing Elements in Cancer Genes
Canson, Daffodil, Dumenil, Troy, Parsons, Michael, O’Mara, Tracy, Davidson, Aimee , Okano, Satomi , Signal, Bethany , Mercer, Tim, Glubb, Dylan and Spurdle, Amanda (2021). The Impact of Variants at Branchpoint Splicing Elements in Cancer Genes. SSRN Electronic Journal, 24 (2), 398-409. doi: 10.2139/ssrn.3933049
2020
Journal Article
Co-existence of leiomyomas, adenomyosis and endometriosis in women with endometrial cancer
Johnatty, Sharon E., Stewart, Colin J. R., Smith, Deborah, Nguyen, Anthony, O’ Dwyer, John, O’Mara, Tracy A., Webb, Penelope M. and Spurdle, Amanda B. (2020). Co-existence of leiomyomas, adenomyosis and endometriosis in women with endometrial cancer. Scientific Reports, 10 (1) 3621. doi: 10.1038/s41598-020-59916-1
2020
Journal Article
Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars
Canson, Daffodil, Glubb, Dylan and Spurdle, Amanda B. (2020). Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Human Mutation, 41 (10) humu.24074, 1705-1721. doi: 10.1002/humu.24074
2019
Journal Article
A functional assay–based procedure to classify mismatch repair gene variants in Lynch syndrome
Drost, Mark, Tiersma, Yvonne, Thompson, Bryony A., Frederiksen, Jane H., Keijzers, Guido, Glubb, Dylan, Kathe, Scott, Osinga, Jan, Westers, Helga, Pappas, Lisa, Boucher, Kenneth M., Molenkamp, Siska, Zonneveld, José B., van Asperen, Christi J., Goldgar, David E., Wallace, Susan S., Sijmons, Rolf H., Spurdle, Amanda B., Rasmussen, Lene J., Greenblatt, Marc S., de Wind, Niels and Tavtigian, Sean V. (2019). A functional assay–based procedure to classify mismatch repair gene variants in Lynch syndrome. Genetics in Medicine, 21 (7), 1486-1496. doi: 10.1038/s41436-018-0372-2
2018
Journal Article
Heritable DNA methylation marks associated with susceptibility to breast cancer
Joo, Jihoon E., Dowty, James G., Milne, Roger L., Wong, Ee Ming, Dugué, Pierre-Antoine, English, Dallas, Hopper, John L., Goldgar, David E., Giles, Graham G., Southey, Melissa C., kConFab, Sexton, Adrienne, Christian, Alice, Trainer, Alison, Spigelman, Allan, Fellows, Andrew, Shelling, Andrew, De Fazio, Anna, Blackburn, Anneke, Crook, Ashley, Meiser, Bettina, Patterson, Briony, Clarke, Christine, Saunders, Christobel, Hunt, Clare, Scott, Clare, Amor, David, Marsh, Deborah, Edkins, Edward ... Antill, Yoland (2018). Heritable DNA methylation marks associated with susceptibility to breast cancer. Nature Communications, 9 (1) 867. doi: 10.1038/s41467-018-03058-6
2018
Journal Article
Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants
Dadaev, Tokhir, Saunders, Edward J., Newcombe, Paul J., Anokian, Ezequiel, Leongamornlert, Daniel A., Brook, Mark N., Cieza-Borrella, Clara, Mijuskovic, Martina, Wakerell, Sarah, Olama, Ali Amin Al, Schumacher, Fredrick R., Berndt, Sonja I., Benlloch, Sara, Ahmed, Mahbubl, Goh, Chee, Sheng, Xin, Zhang, Zhuo, Muir, Kenneth, Govindasami, Koveela, Lophatananon, Artitaya, Stevens, Victoria L., Gapstur, Susan M., Carter, Brian D., Tangen, Catherine M., Goodman, Phyllis, Thompson, Ian M., Batra, Jyotsna, Chambers, Suzanne, Moya, Leire ... The PRACTICAL (Prostate Cancer Association Group to Investigate Cancer-Associated Alterations in the Genome) Consortium (2018). Fine-mapping of prostate cancer susceptibility loci in a large meta-analysis identifies candidate causal variants. Nature Communications, 9 (1) 2256. doi: 10.1038/s41467-018-04109-8
Funding
Past funding
Supervision
Availability
- Honorary Professor Amanda Spurdle is:
- Available for supervision
Before you email them, read our advice on how to contact a supervisor.
Available projects
-
Evaluation of variants in known or candidate high-risk cancer genes
Background: Panel gene testing is increasingly applied to identify the underlying genetic cause of cancer in patients with suspected hereditary cancer. Identification of a pathogenic variant directly influences clinical management for patients and their at-risk relatives, setting the path for preventative and increasingly chemotherapeutic options. Unfortunately, such testing often identifies variants with uncertain impact on function and clinical phenotype. Such variants of uncertain clinical significance create considerable difficulties for counselling and clinical management. A range of methods can be useful for assessing variants, including bioinformatic analysis, assays of mRNA and protein function, and also investigating association with clinical features such as segregation in families, age at onset /phenotype in case-control studies and tumour pathology.
Aim: To use statistical and laboratory methods to assess the clinical relevance of rare cancer gene sequence variants identified by clinical genetic testing of patients with suspected hereditary cancer, identified in Australia or through the international consortia such as ENIGMA.
Approach: This project will assess the effect of variants on gene/protein function using a variety of bioinformatic predictions, molecular biological assays and/or statistical analyses. Techniques may include RNA analyses using LCLs and/or constructs, protein assays in collaboration with other laboratories, pedigree analysis and simple statistical analyses of clinical factors predictive of pathogenic variant status, to develop calibrated measures of association with disease for use in multifactorial likelihood analysis.
Outcome: Analysis of specific variants will provide evidence regarding their pathogenicity for translation in the clinical setting. Comparison of assay results with risk will form the foundation for improving bioinformatic prediction tools and incorporating predictions and/or biological assay results in statistical models of risk prediction.
Supervision history
Current supervision
-
Doctor Philosophy
From Association to Mechanism: Investigating the Functional Role of Endometrial Cancer Risk Variants Identified in GWAS
Associate Advisor
Other advisors: Dr Dylan Glubb
Completed supervision
-
2022
Doctor Philosophy
Bioinformatic and mRNA analysis of germline variants implicated in cancer risk
Principal Advisor
Other advisors: Dr Dylan Glubb
-
2020
Doctor Philosophy
Identification of genetic variants associated with risk of endometrial cancer
Principal Advisor
-
2020
Doctor Philosophy
Classification of germline variants in the TP53 gene: from uncertainty to clinical action
Principal Advisor
-
2014
Doctor Philosophy
Interpreting the clinical significance of mismatch repair gene sequence variants
Principal Advisor
-
2008
Doctor Philosophy
BRCA1 interactors and cancer
Principal Advisor
Other advisors: Honorary Professor Kum Kum Khanna
-
2022
Doctor Philosophy
Next generation sequencing analysis for the diagnosis of suspected hereditary cancer cases
Associate Advisor
-
2014
Doctor Philosophy
Hereditary endometrial cancer: Improving identification and referral of patients with suspected Lynch syndrome
Associate Advisor
Other advisors: Professor Andreas Obermair, Associate Professor Lisa Fitzgerald
Media
Enquiries
For media enquiries about Honorary Professor Amanda Spurdle's areas of expertise, story ideas and help finding experts, contact our Media team: